7apu | pdb_00007apu

Structure of Adenylate kinase from Escherichia coli in complex with two ADP molecules refined at 1.36 A resolution.

spinqualitylabelsall models 7apu, resolution 1.36Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 7apu is a 2 chain structure with sequence from Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: ADP, NA Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function KAD_ECOLI Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. This small ubiquitous enzyme involved in the energy metabolism and nucleotide synthesis, is essential for maintenance and cell growth.[HAMAP-Rule:MF_00235] Publication Abstract from PubMed Enzymes employ a wide range of protein motions to achieve efficient catalysis of chemical reactions. While the role of collective protein motions in substrate binding, product release, and regulation of enzymatic activity is generally understood, their roles in catalytic steps per se remain uncertain. Here, molecular dynamics simulations, enzyme kinetics, X-ray crystallography, and nuclear magnetic resonance spectroscopy are combined to elucidate the catalytic mechanism of adenylate kinase and to delineate the roles of catalytic residues in catalysis and the conformational change in the enzyme. This study reveals that the motions in the active site, which occur on a time scale of picoseconds to nanoseconds, link the catalytic reaction to the slow conformational dynamics of the enzyme by modulating the free energy landscapes of subdomain motions. In particular, substantial conformational rearrangement occurs in the active site following the catalytic reaction. This rearrangement not only affects the reaction barrier but also promotes a more open conformation of the enzyme after the reaction, which then results in an accelerated opening of the enzyme compared to that of the reactant state. The results illustrate a linkage between enzymatic catalysis and collective protein motions, whereby the disparate time scales between the two processes are bridged by a cascade of intermediate-scale motion of catalytic residues modulating the free energy landscapes of the catalytic and conformational change processes. Dynamic Connection between Enzymatic Catalysis and Collective Protein Motions.,Ojeda-May P, Mushtaq AU, Rogne P, Verma A, Ovchinnikov V, Grundstrom C, Dulko-Smith B, Sauer UH, Wolf-Watz M, Nam K Biochemistry. 2021 Jul 20;60(28):2246-2258. doi: 10.1021/acs.biochem.1c00221. , Epub 2021 Jul 12. PMID:34250801 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Adenylate kinase 3D structures

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